Fiji's military regime says it is deporting a Catholic priest who had been the subject of abusive text messages and phone calls by military strongman Voreqe Bainimarama.

Australian Father Kevin Barr is now believed to be inside the Australian High Commission in Suva, seeking protection.

In a brief phone conversation with Fairfax Media, he said "I cannot talk..."

"Our worst fears have eventuated, I am in an awkward position."

Sources in Suva told Fairfax Media that the military tried to set up a meeting with Barr but he instead went to the diplomatic mission.

After the news broke on Stuff, the military's immigration minister Joketani Cokanasiga declared Barr was a "prohibited immigrant due to a breach in his work permit".

"The Department has issued a formal notice to Father Barr who has until Sunday the 27th of January to leave the country."

Barr joins a long list of people who have been deported by Bainimarama, including two New Zealanders and an Australian diplomat, a Fairfax Media reporter and reporters from Television New Zealand and the Australian Broadcasting Corporation.

Barr, who has lived in Fiji for 32 years, was long seen as a Bainimarama supporter but earlier this month he was subjected to a torrent of abuse after he suggested the Chinese flag could replace the Union Jack on Fiji's planned new flag.

But after he made the Chinese crack in a letter to the Fiji Sun, he got a phone call from Bainimarama himself.

"Then in a very angry voice he said that I should apologise to the people of Fiji for my letter concerning the Fijian flag in the newspaper," Barr said in a letter he wrote privately to the Australian High Commission but which has been leaked in blogs.

Barr confirmed to Fairfax Media it was his letter.

"(Bainimarama) then called me 'a f***** up priest' and said I had become anti-government," Barr said.

He repeated the phrase again and threw in a few swear words and told him to go back to where he came from.

"His tone was angry and really over the top."

Minutes later he got a text message from Bainimarama: "I think you owe the people of Fiji an apology for your childish comments. You give all Catholic priests a bad name."

Barr said he replied that he was not anti-government but disappointed at some developments.

He then got a reply from Bainimarama: "F*** U a***hole. Stay well away from me."

Shortly later he got another text telling him to "start saying your goodbyes" and pointing out his work permit expired at the end of the year: "Go and be a missionary in China".